Investigation of G007-LK treatment in mouse and human melanoma cell lines

Introduction

• WNT/β-catenin pathway -> disregulation in melanoma

• G007LK -> decreases WNT/β-catenin signaling

• Two data sets and two metadata sets (mouse and human)

• Goal was to identify up and down regulated genes after G007LK treatment

Methods

Cleaning

• How we cleaned the data and why

Augmentation

• How we processed or data to prepare it for analysis
• Why we did 0 handling and how
• Why we did log2 fold expressions

Description (1)

• Many zero expressions through cell lines in each of treatment

Description (2)

Results

Mouse gene expression analysis

• Only 346 significantly regulated genes out of 39075
• 0 handling making estimated treatment impact on expressions unsure.

Analysis of regulated Mouse genes across the 3 treatments

• Approximately equal amounts of significantly regulated genes in each treatment

• However, the overlap is very small

Discussion

The Human Analysis

• PCA analysis across 18 human cell lines

Discussion

• In our mouse model, the BVES gene appears to be the most significantly impacted.This gene contributes to regeneration processes

• Our holistic investigation across mouse and human melanoma cell lines provided valuable insights into the influences of the studied compounds and G007.LK effects on their gene expression patterns

• More extensive work is needed to fully understand the impact of the G007.LK in gene expression and cellular pathway across different melanoma cells

References

Jo Waaler (2022) Human melanoma cell lines treated with G007-LK. BioStudies, E-MTAB-8438. Retrieved from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-8438

Jo Waaler (2021). Mouse melanoma cell line B16-F10 treated with G007-LK. BioStudies, E-MTAB-8101. Retrieved from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-8101

Waaler, Jo, et al. “Tankyrase Inhibition Sensitizes Melanoma to PD-1 Immune Checkpoint Blockade in Syngeneic Mouse Models.” Communications Biology, vol. 3, no. 1, 24 Apr. 2020, https://doi.org/10.1038%2Fs42003-020-0916-2 Accessed 25 Nov. 2023

Martín‐Fernández, Josep Antoni, Javier Palarea‐Albaladejo, and Ricardo Antonio Olea. “Dealing with zeros.” Compositional data analysis: Theory and applications (2011): 43-58.